Gene Page: NOTCH4

Summary ?
GeneID4855
SymbolNOTCH4
SynonymsINT3
Descriptionnotch 4
ReferenceMIM:164951|HGNC:HGNC:7884|Ensembl:ENSG00000204301|HPRD:01290|Vega:OTTHUMG00000031044
Gene typeprotein-coding
Map location6p21.3
Pascal p-value1E-12
Sherlock p-value0.15
Fetal beta-0.546
DMG1 (# studies)
eGeneMyers' cis & trans
Meta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies2Link to SZGene
GSMA_IGenome scan meta-analysisPsr: 0.033 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg26950898632164380NOTCH49.49E-8-0.0072.14E-5DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7132043chr1280968399NOTCH448550.19trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
NPY5R0.760.86
PROM10.750.63
NPNT0.750.62
GRAP20.740.59
MARCH10.740.82
ARHGAP150.730.60
LMO40.730.84
AC079061.10.720.84
GRM70.720.79
RBM240.720.83
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
REEP6-0.50-0.47
UBTD1-0.48-0.59
HSD17B14-0.47-0.63
RHBDL3-0.46-0.59
AIFM3-0.46-0.57
TSC22D4-0.45-0.58
S100B-0.45-0.59
BDH2-0.44-0.59
ACSF2-0.44-0.64
RENBP-0.44-0.52

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004872receptor activityTAS11823422 
GO:0005509calcium ion bindingIEA-
GO:0005509calcium ion bindingTAS11823422 
GO:0005515protein bindingIPI7671825 
GO:0046982protein heterodimerization activityTAS8681805 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001569patterning of blood vesselsISS-
GO:0001709cell fate determinationTAS11823422 
GO:0001763morphogenesis of a branching structureISS-
GO:0006350transcriptionIEA-
GO:0007219Notch signaling pathwayIEA-
GO:0009790embryonic developmentISS-
GO:0007275multicellular organismal developmentIEA-
GO:0030154cell differentiationIEA-
GO:0030879mammary gland developmentIDA9576833 
GO:0050793regulation of developmental processIEA-
GO:0030097hemopoiesisTAS11532344 
GO:0045602negative regulation of endothelial cell differentiationISS-
GO:0045893positive regulation of transcription, DNA-dependentTAS11823422 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusTAS8681805 
GO:0016020membraneIEA-
GO:0016021integral to membraneIEA-
GO:0009986cell surfaceIDA11823422 
GO:0005886plasma membraneIEA-
GO:0005887integral to plasma membraneTAS11823422 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG DORSO VENTRAL AXIS FORMATION 2521All SZGR 2.0 genes in this pathway
KEGG NOTCH SIGNALING PATHWAY 4735All SZGR 2.0 genes in this pathway
PID NOTCH PATHWAY 5949All SZGR 2.0 genes in this pathway
REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION 2917All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY NOTCH4 1210All SZGR 2.0 genes in this pathway
REACTOME PRE NOTCH EXPRESSION AND PROCESSING 4424All SZGR 2.0 genes in this pathway
REACTOME PRE NOTCH PROCESSING IN GOLGI 1610All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY 352181All SZGR 2.0 genes in this pathway
REACTOME NOTCH HLH TRANSCRIPTION PATHWAY 138All SZGR 2.0 genes in this pathway
REACTOME RECEPTOR LIGAND BINDING INITIATES THE SECOND PROTEOLYTIC CLEAVAGE OF NOTCH RECEPTOR 128All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY NOTCH 10364All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
LIU CDX2 TARGETS UP 3622All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN 770415All SZGR 2.0 genes in this pathway
WANG ESOPHAGUS CANCER VS NORMAL UP 12172All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK DN 196131All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS UP 169127All SZGR 2.0 genes in this pathway
THEODOROU MAMMARY TUMORIGENESIS 3124All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX 230156All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 7 2722All SZGR 2.0 genes in this pathway
DING LUNG CANCER MUTATED FREQUENTLY 1210All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP 398262All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP 207145All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
GOLDRATH IMMUNE MEMORY 6542All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 6HR DN 2113All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY UP 8648All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL 254164All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 24HR 2013All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN 216143All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS UP 165118All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435289All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 LCP WITH H3K4ME3 16280All SZGR 2.0 genes in this pathway
MIKKELSEN IPS LCP WITH H3K4ME3 174100All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
MIKKELSEN ES LCP WITH H3K4ME3 14280All SZGR 2.0 genes in this pathway
FUKUSHIMA TNFSF11 TARGETS 1614All SZGR 2.0 genes in this pathway
KOHOUTEK CCNT2 TARGETS 5835All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES 462273All SZGR 2.0 genes in this pathway
DURAND STROMA S UP 297194All SZGR 2.0 genes in this pathway